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Yorodumi- PDB-7sgf: Lassa virus glycoprotein construct (Josiah GPC-I53-50A) in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7sgf | ||||||
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Title | Lassa virus glycoprotein construct (Josiah GPC-I53-50A) in complex with LAVA01 antibody | ||||||
Components |
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Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / glycoprotein / Lassa / Josiah / vaccine design / nanoparticle / protein design / VIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||
Function / homology | Function and homology information host cell Golgi membrane / receptor-mediated endocytosis of virus by host cell / host cell endoplasmic reticulum membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Lassa mammarenavirus Oryctolagus cuniculus (rabbit) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.41 Å | ||||||
Authors | Antanasijevic, A. / Brouwer, P.J.M. / Ward, A.B. | ||||||
Funding support | United States, 1items
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Citation | Journal: Cell Host Microbe / Year: 2022 Title: Lassa virus glycoprotein nanoparticles elicit neutralizing antibody responses and protection. Authors: Philip J M Brouwer / Aleksandar Antanasijevic / Adam J Ronk / Helena Müller-Kräuter / Yasunori Watanabe / Mathieu Claireaux / Hailee R Perrett / Tom P L Bijl / Marloes Grobben / Jeffrey C ...Authors: Philip J M Brouwer / Aleksandar Antanasijevic / Adam J Ronk / Helena Müller-Kräuter / Yasunori Watanabe / Mathieu Claireaux / Hailee R Perrett / Tom P L Bijl / Marloes Grobben / Jeffrey C Umotoy / Angela I Schriek / Judith A Burger / Khadija Tejjani / Nicole M Lloyd / Thijs H Steijaert / Marlies M van Haaren / Kwinten Sliepen / Steven W de Taeye / Marit J van Gils / Max Crispin / Thomas Strecker / Alexander Bukreyev / Andrew B Ward / Rogier W Sanders / Abstract: The Lassa virus is endemic in parts of West Africa, and it causes hemorrhagic fever with high mortality. The development of a recombinant protein vaccine has been hampered by the instability of ...The Lassa virus is endemic in parts of West Africa, and it causes hemorrhagic fever with high mortality. The development of a recombinant protein vaccine has been hampered by the instability of soluble Lassa virus glycoprotein complex (GPC) trimers, which disassemble into monomeric subunits after expression. Here, we use two-component protein nanoparticles consisting of trimeric and pentameric subunits to stabilize GPC in a trimeric conformation. These GPC nanoparticles present twenty prefusion GPC trimers on the surface of an icosahedral particle. Cryo-EM studies of GPC nanoparticles demonstrated a well-ordered structure and yielded a high-resolution structure of an unliganded GPC. These nanoparticles induced potent humoral immune responses in rabbits and protective immunity against the lethal Lassa virus challenge in guinea pigs. Additionally, we isolated a neutralizing antibody that mapped to the putative receptor-binding site, revealing a previously undefined site of vulnerability. Collectively, these findings offer potential approaches to vaccine and therapeutic design for the Lassa virus. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7sgf.cif.gz | 364.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7sgf.ent.gz | 266.2 KB | Display | PDB format |
PDBx/mmJSON format | 7sgf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sg/7sgf ftp://data.pdbj.org/pub/pdb/validation_reports/sg/7sgf | HTTPS FTP |
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-Related structure data
Related structure data | 25109MC 7sgdC 7sgeC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 1 types, 6 molecules AaBbCc
#1: Protein | Mass: 73845.570 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lassa mammarenavirus / Plasmid: pPPI4 / Cell (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q6GWS0 |
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-Antibody , 2 types, 6 molecules HJMLKN
#2: Antibody | Mass: 15459.241 Da / Num. of mol.: 3 / Fragment: Fab fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Plasmid: pPPI4 / Cell (production host): HEK293F / Production host: Homo sapiens (human) #3: Antibody | Mass: 12490.637 Da / Num. of mol.: 3 / Fragment: Fab fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Plasmid: pPPI4 / Cell (production host): HEK293F / Production host: Homo sapiens (human) |
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-Sugars , 6 types, 33 molecules
#4: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #5: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #6: Polysaccharide | Source method: isolated from a genetically manipulated source #7: Polysaccharide | Source method: isolated from a genetically manipulated source #8: Polysaccharide | Source method: isolated from a genetically manipulated source #9: Sugar | ChemComp-NAG / |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Lassa virus glycoprotein construct(Josiah GPC-I53-50A) in complex with LAVA01 antibody (as Fab fragment) Type: COMPLEX Details: Complex was assembled by combining GPC-I53-50A and LAVA01 Fabs Entity ID: #1-#3 / Source: MULTIPLE SOURCES | |||||||||||||||
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Molecular weight | Experimental value: NO | |||||||||||||||
Source (natural) | Organism: Lassa mammarenavirus | |||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) / Cell: HEK293F | |||||||||||||||
Buffer solution | pH: 7 / Details: TBS | |||||||||||||||
Buffer component |
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Specimen | Conc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: The complex was assembled by combining chemically cross-linked GPC-I53-50A with 6-fold molar excess of LAVA01 antibody (as Fab fragment). | |||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3 | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 K / Details: Blot time 5s, Wait time 10s, Blot force 0 |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 29000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 9.5 sec. / Electron dose: 50.3 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3098 |
Image scans | Movie frames/image: 38 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 416326 / Details: template picker | ||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C3 (3 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.41 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8480 / Algorithm: BACK PROJECTION Details: C3 symmetry was used for refinement. Solvent mask around the complex was used for refinement. Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 5VK2 |